Defour is facing at least two months on the sidelines after scans revealed he needs surgery on a knee injury.
The 29-year-old Belgian was ruled out of Wednesday night's Premier League trip to Newcastle and he will now undergo an operation to repair cartilage damage.
"Scans showed the Clarets' midfielder must undergo surgery to repair cartilage damage. Defour, 29, had been an ever-present for Burnley in the Premier League this season.
No timeframe has been placed on Heaton's return to action with Michael Duff's side and the 31-year-old has only recently returned to training with the rest of the goalkeeping group.
Heaton has been out of action since dislocating his shoulder in the win over Crystal Palace on September 10.
Asked if his skipper will feature for Duff's side, Dyche said: "Definitely. I think it's different the other way for a goalkeeper. I think they need games.
"Outfield players, particularly strikers, you want them almost off the cuff a little bit.
"Defenders like to get their eye in, goalkeepers like to get their eye in, that game-ready feel. I think that's important. So he'll definitely play games, when he's ready, of course. And he'll want to. I know Tom. I know what he's like. He will definitely want to play games."